So I finally broke down and decided to track down my rear window issue. I could raise it and lower it from inside but only raise it from the rear key switch. I took apart all the internal panels following the wires from the relay box to the switch in the tail gate. Couldn't find anything wrong. Then I took apart the rear switch cleaned it and put it back. Using the ohm meter I thought it was the switch for some reason. I don't know why maybe I miss used the meter because it didn't fix the problem. Last placed I checked was the Relay Box. Should have checked there first cause the bottom of the circuit board had that nasty blue stuff that build around the battery terminals. It was all over the bottom board. The line that tells it to go down from the back is the line on the bottom of the circuit board it was toast. so after a quick sodder hack I was back and running. That rear window causes so many problems.

Interesting...I'm not sure what you're saying about the rear switch in the back to raise and lower the window though...but my switch in the center console won't lower/raise my rear window, either. After some voltage readings, I determined power was getting TO the switch so...hey, switch right? Wrong (And it was $35 from Toyota, too). Frustrated, I got a wire and started jumping each of the 5 possible contacts in the terminal harness going to the switch...and discovered I can lower and raise the window by 2 unique sets of contacts....?? I ccould re-wire the switch...but I'd sure like it to work like it was suppose to, ya know. Your problem sounded like there was no way this would have worked though, right?

I'm calling the key hole in the tailgate the rear switch.

Not sure how much you know about the window and all the things that can keep it from going up or down. You may have the window lock button engaged and not know it. Or if you have the rear wipper on it wont go. Or even if you have the rear wiper on and the connection to the wipper disconnected it wont go up or down. Or the switch that lets you know if the top is on or.... getting the rear window to work can be an electrical headache.

The FSM has a diagram on how all the the thing is wired up.

I have the diagram and most of the troubleshooting section on my web page:

http://www.4crawler.com/4x4/CheapTricks/RearWindow.shtml